Genome informatics 2008 : proceedings of the 19th International Conference, Gold Coast, Queensland, Australia, 1-3 December 2008 / editors, Jonathan Arthur, See-Kiong Ng. — London : Singapore ; Hackensack, NJ : Imperial College Press ; Distributed by

Contents

    CONTENTS
    
    Preface
    Acknowledgments
    Committees
    Part A Full Papers
    An Approach to Transcriptome Analysis of Non-Model Organisms Using Short-Read Sequences
    Factoring Local Sequence Composition in Motif Significance Analysis
    A New Model of Multi-Marker Correlation for Genome-Wide Tag SNP Selection
    Phenotype Profiling of Single Gene Deletion Mutants of E. coli Using Biolog Technology
    Improved Algorithms for Enumerating Tree-Like Chemical Graphs with Given Path Frequency
    BSAlign: A Rapid Graph-Based Algorithm for Detecting Ligand- Binding Sites in Protein Structures
    Protein Complex Prediction Based on Mutually Exclusive Interactions in Protein Interaction Network
    On the Reconstruction of the Mus musculus Genome-Scale Metabolic Network Model
    Predicting Differences in Gene Regulatory Systems by State Space Models 101
    Exploratory Simulation of Cell Ageing Using Hierarchical Models 114
    Inferring Differential Leukocyte Using a Latent Variable Model
    Activity from Antibody Microarrays
    Assessing and Predicting Protein Interactions Using Both Local and Global Network Topological Metrics 138
    Modelling the Evolution of Protein Coding Sequences Sampled from Measurably Evolving Populations 150
    A Phylogenomic Approach for Studying Plastid Endosymbiosis
    Cis-Regulatory Element Based Gene Finding: An Application in Arabidopsis thaliana
    Using Simple Rules on Presence and Positioning of Motifs for Promoter Structure Modeling and Tissue-Specific Expression Prediction 188
    Improving Gene Expression Cancer Molecular Pattern Discovery Using Nonnegative Principal Component Analysis
    Simulation Analysis for the Effect of Light-Dark Cycle on the Entrainment in Circadian Rhythm
    Part B Keynote Addresses
    Sequencing the Transcriptome in toto
    Modern Homology Search
    Modeling Human Genome-Wide Combinatorial Regulatory Networks Initiated by Transcription Factors and microRNAs Using Forward and Reverse Engineering 230
    Reconstructing the Circuits of Disease: From Molecular States to Physiological States 231
    The Emerging Generalizations of Prokaryotic Genomics
    A New Understanding of the Human Genome
    Author Index